Well, perhaps the Pokeballs in this fanfic could be like the Command Spells in Fate Stay Night. A trainer might use a Pokeball to summon and control a powerful 'Pokemon - Servant' hybrid. And the different regions in the Pokemon world could be the battlefields for the Grail War. The trainers would travel around, catching and training their unique Pokemon - Servants while competing for the Grail.
In this fanfic, the Pokedex could be a magical book that not only records Pokemon - Servants' information but also their hidden powers. The story could involve a young trainer who discovers that he has a special connection to the Fate Stay Night world. He starts his journey to gather the most powerful Pokemon - Servants to win the Grail War. Along the way, he has to face other trainers with their own strategies and Pokemon - Servant teams.
Another idea is to create a story where the rules of the Grail War are changed. For instance, instead of seven Servants, there are only three, and they have to complete different tasks to win. This would completely change the dynamics of the story and lead to new and exciting interactions between the characters.
A plot could be that Mordred is summoned by a powerful ninja as a last - ditch effort to fight against an ancient evil that has emerged in the Naruto world. This evil has powers similar to some of the powerful Servants in Fate Stay Night, so Mordred's expertise is needed.
One idea could be to have Naruto characters participate in the Holy Grail War. For example, Naruto himself could be a Servant, perhaps with his chakra being a unique form of mana. His skills like the Rasengan could be reimagined as powerful Noble Phantasms. Another idea is to put the Fate Stay Night characters in the Naruto world. They might have to deal with things like ninja clans and the politics of the hidden villages while also trying to find a way back to their own world.
One idea could be exploring Archer's internal struggle more deeply. Maybe show his memories of past battles and how they affect his decisions in the Fourth War. Another could be to create a scenario where Archer has to team up with an unexpected character from the Fate universe.
One interesting idea could be exploring different routes for the characters. For example, what if Shirou had chosen a different Servant at the start? Another could be delving deeper into the backstories of the Servants, like revealing more about their lives before they became heroic spirits. Some fanfictions also play with the concept of alternate universes, where the rules of the Holy Grail War are changed completely.
Another interesting plot might be a 'what if' scenario. What if Shirou had to enter Rider's world, like the world she came from before being summoned in Fate Stay Night? He would be completely out of his element, and Rider would have to be his guide. This could lead to many comical and heart - warming moments as Shirou tries to adapt and they grow closer.
One interesting plot idea could be that the Servants from Fate Stay Night end up in the Naruto world. For example, Saber could team up with Naruto. Saber's noble and just nature would blend well with Naruto's determination to protect his village. They could face off against common enemies like Orochimaru, who might be interested in the power of the Servants. Another idea is that the concept of chakra in the Naruto world could interact with the magic in Fate Stay Night. Maybe a mage from the Fate universe tries to study chakra and finds a way to combine it with their own magic system, creating a whole new type of power. A third plot could involve the Holy Grail War taking place in the Hidden Leaf Village. The ninjas would be both intrigued and cautious about this strange new event, and the Servants would have to navigate the politics and unique environment of the village while fighting for the Grail.
One idea could be that Saber from 'Fate Stay Night' gets transported to the world of 'Frozen'. She could be mistaken for a powerful sorceress. Elsa might initially be wary of her but then realize they both have a connection to magic that they need to control. Another plot could involve Shirou being in Arendelle and using his skills to help build things, while also getting caught up in the drama between Anna and Hans. Maybe he could use his projection magic to create something that helps save the day in Arendelle.
A cool 'fate stay night crossover fanfiction' idea might be a crossover with 'Final Fantasy'. The different classes and magic systems in Final Fantasy could blend well with the Fate universe. For example, a character from Fate could learn the job classes from Final Fantasy. Also, a crossover with 'Persona' could be interesting. The Velvet Room and the concept of personas could be integrated into the Fate world, adding a new layer of mystery and power to the story.
One idea could be exploring the backstories of the minor characters in more depth. For example, the story could focus on how a certain side character got involved in the Holy Grail War in the first place. Another plot could be a what - if scenario, like what if Shirou had made different choices during key moments in the original story. It could also be interesting to see a story from the perspective of the Servants' lives before being summoned to the Grail War.